Side chain conformation tertiary protein structure

MD production runs are just a continuation of the MD equilibrium and continue up to several nanoseconds. The results from the production runs can be used for docking studies or to determine changes in the secondary or tertiary structure of the target protein. Protein models refined with MD simulations consist of a library of structures with similar backbone geometry, but with different side-chain rotamers. These different structures are especially useful for molecular docking studies when the conformation of the protein and the orientation of the side chains are unknown. 

When the urea and thiol are removed by dialysis (see p. 78), secondary and tertiary structures develop again spontaneously. The cysteine residues thus return to a suf ciently close spatial vicinity that disulfide bonds can once again form under the oxidative effect of atmospheric oxygen. The active center also reestablishes itself In comparison with the denatured protein, the native form is astonishingly compact, at 4.5 2.5 nm. In this state, the apolar side chains (yellow) predominate in the interior of the protein, while the polar residues are mainly found on the surface. This distribution is due to the hydrophobic effect (see p. 28), and it makes a vital contribution to the stability of the native conformation (B). 

The biological function of peptides and proteins depends on their native conformation. The side-chain functionalities of the a-amino acids that comprise peptides and proteins have profound effects on their properties. These functionalities reside in the 20 naturally occurring a-amino acids, which have different propensities for formation of the three major secondary structural conformations. 1 In addition to these naturally occurring a-amino acids whose primary structure enables the polypeptide to fold into a predictable secondary and tertiary structure, the incorporation of unnatural amino acids has opened important areas of research. 

Another major effect, found in PGA, is optical inversion of L-glutamate to D-glutamate residues. One implication of the radiation-induced optical inversion in proteins is that some modification of amino acids may pass undetected by the usual chemical analyses which do not distinguish between l- and D-isomers. Furthermore, introducing a D-amino acid residue into a protein could have a far-reaching effect on the secondary and tertiary structures, and this could have a more serious effect on the functional properties of the molecule than changes in the side chains. One biological property of PGA which is affected by irradiation in solution is its hydrolysis by proteolytic enzymes. The conformation of the polymer has a marked effect on its susceptibility to hydrolysis by certain enzymes 27), and we have... 

The properties of a protein depend primarily on its three-dimensional structure. The sequence of amino acids in the polypeptide chain is termed its primary structure. Its secondary structure is the shape of the backbone polypeptide chain. Remember that each amide group is planar, but the chain can have various conformations about the bond between the a-carbon and the nitrogen. The tertiary structure is the overall three-dimensional shape of the protein, including the conformations of the side chains. 

The conformation of a protein in a particular environment affects its functional properties. Conformation is governed by the amino acid composition and their sequence as influenced by the immediate environment. The secondary, tertiary and quaternary structures of proteins are mostly due to non-covalent interactions between the side chains of contiguous amino acid residues. Covalent disulfide bonds may be important in the maintenance of tertiary and quaternary structure. The non-covalent forces are hydrogen bonding, electrostatic interactions, Van der Waals interactions and hydrophobic associations. The possible importance of these in relation to protein structure and function was discussed by Ryan (13). 

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